User:Eric Martz/Sandbox 8
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< User:Eric Martz(Difference between revisions)
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| + | ==Chemistry of Water and Its Hydrogen Bonds== | ||
| + | Prepared in collaboration with [[User:Gabriel Pons]]. | ||
| + | |||
| + | ===One Molecule=== | ||
<applet size='400' frame='true' align='right' caption='Insert caption here' | <applet size='400' frame='true' align='right' caption='Insert caption here' | ||
scene='User:Eric_Martz/Sandbox_8/Water/2' /> | scene='User:Eric_Martz/Sandbox_8/Water/2' /> | ||
*(<scene name='User:Eric_Martz/Sandbox_8/Water/2'>restore initial scene</scene>) | *(<scene name='User:Eric_Martz/Sandbox_8/Water/2'>restore initial scene</scene>) | ||
| - | *<scene name='User:Eric_Martz/Sandbox_8/Water/3'>partial charges</scene> (using δ in the label, it gets corrupted) | ||
*<scene name='User:Eric_Martz/Sandbox_8/Water/4'>partial charge values</scene> | *<scene name='User:Eric_Martz/Sandbox_8/Water/4'>partial charge values</scene> | ||
*<scene name='User:Eric_Martz/Sandbox_8/Water/6'>shape of the molecule (spacefilling)</scene> (van der Waals radii) | *<scene name='User:Eric_Martz/Sandbox_8/Water/6'>shape of the molecule (spacefilling)</scene> (van der Waals radii) | ||
*<scene name='User:Eric_Martz/Sandbox_8/Water/5'>translucent surface colored by molecular electrostatic potential</scene> <font color="blue"><b>Positive (+)</b></font>, <font color="red"><b>Negative (-)</b></font> | *<scene name='User:Eric_Martz/Sandbox_8/Water/5'>translucent surface colored by molecular electrostatic potential</scene> <font color="blue"><b>Positive (+)</b></font>, <font color="red"><b>Negative (-)</b></font> | ||
| + | |||
| + | ---- | ||
| + | ===Technical Information=== | ||
| + | |||
| + | The following scene demonstrates a problem with greek letters in labels in Jmol | ||
| + | *<scene name='User:Eric_Martz/Sandbox_8/Water/3'>partial charges</scene> (using δ in the label, it gets corrupted) | ||
Script for translucent MEP colored surface: | Script for translucent MEP colored surface: | ||
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# {*}.partialCharge = {*}.temperature.all | # {*}.partialCharge = {*}.temperature.all | ||
| + | </pre> | ||
| + | |||
| + | Possible script for large translucent hbonds: | ||
| + | <pre> | ||
| + | select all | ||
| + | calculate hbonds | ||
| + | hbonds 0.3 | ||
| + | color hbonds white | ||
| + | color hbonds translucent 6 | ||
</pre> | </pre> | ||
Current revision
Chemistry of Water and Its Hydrogen Bonds
Prepared in collaboration with User:Gabriel Pons.
One Molecule
|
- ()
- (van der Waals radii)
- Positive (+), Negative (-)
Technical Information
The following scene demonstrates a problem with greek letters in labels in Jmol
- (using δ in the label, it gets corrupted)
Script for translucent MEP colored surface:
{hydrogen}.partialCharge = 0.41
{oxygen}.partialCharge = -0.82
# IMPORTANT: the SOLVENT version of isosurface
# IGNORES WATER UNCONDITIONALLY! We must us MOLECULAR!
#isosurface resolution 6 MOLECULAR colorscheme "rwb" map MEP
isosurface resolution 6 MOLECULAR map MEP
# Higher values of resolution make a choppier surface that rotates
# more jerkily. 6 is good.
color isosurface "rwb" range -0.2 0.2
# chose this range by trial and error.
# default is -0.1 0.1 as reported by the isosurface command.
color isosurface translucent 2
# or the partial charges could be in the PDB file using
# this command to transfer the values.
# {*}.partialCharge = {*}.temperature.all
Possible script for large translucent hbonds:
select all calculate hbonds hbonds 0.3 color hbonds white color hbonds translucent 6
